Re: [Samtools-help] samTools on solaris 10

[Duhaime J. <Joh...@ir...>]

Hello

Error Reading file:

It seems that is because the input file et too big. I really have to compile in 64 bits.

I made a test copying part of the input file:
10,000,000 lines
> ./samtools view -bSt allMM9.fa.fai s_3out10000000.sam > s_3_bam
[samopen] SAM header is present: 22 sequences.

20,000,000 lines
> ./samtools view -bSt allMM9.fa.fai s_3out20000000.sam  > s_3_bam
[main_samview] fail to open file for reading.

15,000,000 lines
> ./samtools view -bSt allMM9.fa.fai s_3out15000000.sam  > s_3_bam
[main_samview] fail to open file for reading.

12,000,000
> ./samtools view -bSt allMM9.fa.fai s_3out12000000.sam  > s_3_bam
[samopen] SAM header is present: 22 sequences.



Compiling:
Still struggling on that.




De : Davide Cittaro [mailto:dav...@if...]
Envoyé : 21 juin 2010 12:11
À : Duhaime Johanne
Cc : sam...@li...
Objet : Re: [Samtools-help] samTools on solaris 10


On Jun 21, 2010, at 5:58 PM, Duhaime Johanne wrote:


Reading the file:

> /apps/programs/samtools faidx mm9.fa
> ls -l mm9.fa.fai
-rw-r--r--   1 duhaimj  si            21 Jun 21 10:50 mm9.fa.fai
> ls -l s_3.sam
-rwxrwxrwx   1 duhaimj  si       5053665320 Jun 14 16:26 s_3.sam
> /apps/programs/samtools view -bt mm9.fa.fai s_3.sam > s_3.bam
[main_samview] fail to open file for reading.

But... is s_3.sam in your cwd? :-)




Running the provided 64 bits binary:
# crle -64

Default configuration file (/var/ld/64/ld.config) not found
  Default Library Path (ELF):   /lib/64:/usr/lib/64  (system default)
  Trusted Directories (ELF):    /lib/secure/64:/usr/lib/secure/64  (system default)

 ./samtools
ld.so.1: samtools: fatal: libz.so.1: version `ZLIB_1.2.2' not found (required by file samtools)
ld.so.1: samtools: fatal: libz.so.1: open failed: No such file or directory
Killed


Missing 64-bit libz may be solution to your issue in building?


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: dav...@if...<mailto:dav...@if...>
*/